1PGJ | pdb_00001pgj

X-RAY STRUCTURE OF 6-PHOSPHOGLUCONATE DEHYDROGENASE FROM THE PROTOZOAN PARASITE T. BRUCEI

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PGD	SHEEP DIMER - SEE PDB ENTRY 2PGD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7		CRYSTALLISED FROM HANGING DROP WHICH ALSO CONTAINED 50MM POTASSIUM PHOSPHATE, 5MM DTT AND 30% SATURATED AMMONIUM SULPHATE, PH 7.0. THE WELL SOLUTION WAS 45% SATURATED AMMONIUM SULPHATE., vapor diffusion - hanging drop

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.13	α = 90
b = 135.13	β = 90
c = 116.74	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	IMAGE PLATE	MARRESEARCH	COLLIMATOR, DUAL SLITS	1992-11-26	M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH2R

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.8	20	95.9	0.099	17.9	7.2		29373

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	SEE JRNL REFERENCE	SHEEP DIMER - SEE PDB ENTRY 2PGD	2.82	19.76	29307	1436	97.7	0.186	0.186	0.2	0.273	RANDOM	26.5

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]

RMS Deviations
Key	Refinement Restraint Deviation
x_mcangle_it	4.49
x_scangle_it	4.49
x_mcbond_it	2.89
x_scbond_it	2.89
x_angle_deg	1.7
x_bond_d	0.013
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d
x_improper_angle_d_na
x_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7302
Nucleic Acid Atoms
Solvent Atoms	129
Heterogen Atoms	20

Software

Software
Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
MOSFLM	data reduction
SSM	data scaling
X-PLOR	phasing